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<li class="navelem"><a class="el" href="dir_2312589fb962dec58b1579fafe6a300a.html">cudamapper</a></li><li class="navelem"><a class="el" href="dir_46ada5e69ffe047ce1b425fcb02bc946.html">include</a></li><li class="navelem"><a class="el" href="dir_00faf102fbd78ece25aa2d8f2597f59b.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_5d9177f36fbce0c085b11d352d248d8a.html">cudamapper</a></li>  </ul>
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<div class="title">overlapper.hpp</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160; </div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;thrust/device_vector.h&gt;</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="preprocessor">#include &quot;index.hpp&quot;</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="preprocessor">#include &quot;types.hpp&quot;</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160; </div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="keyword">namespace </span>claragenomics</div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;{</div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160; </div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="keyword">namespace </span>cudamapper</div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;{</div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160; </div>
<div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">   27</a></span>&#160;<span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;{</div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">~Overlapper</a>() = <span class="keywordflow">default</span>;</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160; </div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">get_overlaps</a>(std::vector&lt;Overlap&gt;&amp; overlaps,</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;                              thrust::device_vector&lt;Anchor&gt;&amp; anchors,</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;                              <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>&amp; index_query,</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;                              <span class="keyword">const</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>&amp; index_target) = 0;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160; </div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">print_paf</a>(<span class="keyword">const</span> std::vector&lt;Overlap&gt;&amp; overlaps);</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160; </div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">filter_overlaps</a>(std::vector&lt;Overlap&gt;&amp; filtered_overlaps, <span class="keyword">const</span> std::vector&lt;Overlap&gt;&amp; overlaps, <span class="keywordtype">size_t</span> min_residues = 5,</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;                                <span class="keywordtype">size_t</span> min_overlap_len = 0);</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;};</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;<span class="comment">//}</span></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;} <span class="comment">// namespace cudamapper</span></div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160; </div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="agroup__cudamapper_html_gab0e3be4a9442dfb2b7952fb473e591a3"><div class="ttname"><a href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">claragenomics::cudamapper::Overlapper::get_overlaps</a></div><div class="ttdeci">virtual void get_overlaps(std::vector&lt; Overlap &gt; &amp;overlaps, thrust::device_vector&lt; Anchor &gt; &amp;anchors, const Index &amp;index_query, const Index &amp;index_target)=0</div><div class="ttdoc">returns overlaps for a set of reads</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Index_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></div><div class="ttdoc">Index - manages mapping of (k,w)-kmer-representation and all its occurences.</div><div class="ttdef"><b>Definition:</b> index.hpp:31</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1Overlapper_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></div><div class="ttdef"><b>Definition:</b> overlapper.hpp:27</div></div>
<div class="ttc" id="agroup__cudamapper_html_ga54fedd97206ad1691f7b9d9966d01371"><div class="ttname"><a href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">claragenomics::cudamapper::Overlapper::print_paf</a></div><div class="ttdeci">static void print_paf(const std::vector&lt; Overlap &gt; &amp;overlaps)</div><div class="ttdoc">prints overlaps to stdout in PAF format</div></div>
<div class="ttc" id="agroup__cudamapper_html_ga3e5732f34489315ec8d1ef8b82ccea5c"><div class="ttname"><a href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">claragenomics::cudamapper::Overlapper::filter_overlaps</a></div><div class="ttdeci">static void filter_overlaps(std::vector&lt; Overlap &gt; &amp;filtered_overlaps, const std::vector&lt; Overlap &gt; &amp;overlaps, size_t min_residues=5, size_t min_overlap_len=0)</div><div class="ttdoc">removes overlaps which are unlikely to be true overlaps</div></div>
<div class="ttc" id="agroup__cudamapper_html_ga569c8855bdf9806d3747b26fc7e98975"><div class="ttname"><a href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">claragenomics::cudamapper::Overlapper::~Overlapper</a></div><div class="ttdeci">virtual ~Overlapper()=default</div><div class="ttdoc">Virtual destructor for Overlapper.</div></div>
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